First, MODELLER is used to generate initial structures for the individual components where reliable templates are available. Then, IMP / PMI is used to model these components using the DSS/EDC crosslinks and the affinity purification data for the entire SEA complex.
A full description of the scripts can be found in Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway.
List of files and directories:
pdbcontains all input structures that were generated by MODELLER or deposited in PDB.
sj_SEA_multi_layers.pyThe main modeling script with 1:3 stoichiometry and rotational symmetry
chimera_scripts/sea_density.cmdChimera script to view all localization density files
MODELLER/Npr2MODELLER scripts to generate comparative models of Npr2
MODELLER/Npr3MODELLER scripts to generate comparative models of Npr3
MODELLER/SEA1MODELLER scripts to generate comparative models of SEA1
MODELLER/SEA2MODELLER scripts to generate comparative models of SEA2
MODELLER/SEA3MODELLER scripts to generate comparative models of SEA3
MODELLER/SEA4MODELLER scripts to generate comparative models of SEA4
outputs/pdbsthe production will write the best scoring models into pdb files they are initialized and then updated as long as the calculation goes (They are the best 500 models, so at the beginning they are empty, since you haven't start the calculation yet)
outputs/rmfsthe production will write the rmf3 files for lowest temperature replica.
stat.n.outlog files. They contain all relevant numbers of the calculation.
Running the MODELLER scripts:
mod9.12 scripts/MODELLER/Npr2/all_sjkim_final1.py: Npr2 9-127
mod9.12 scripts/MODELLER/Npr2/all_sjkim_final2.py: Npr2 257-327
mod9.12 scripts/MODELLER/Npr2/all_sjkim_final3.py: Npr2 563-610
mod9.12 scripts/MODELLER/Npr3/all_sjkim_final1.py: Npr3 322-438
mod9.12 scripts/MODELLER/Npr3/all_sjkim_final2.py: Npr3 531-577
mod9.12 scripts/MODELLER/Npr3/all_sjkim_final3.py: Npr3 1-31
mod9.12 scripts/MODELLER/Npr3/all_sjkim_final4.py: Npr3 950-988
mod9.12 scripts/MODELLER/Npr3/all_sjkim_final5.py: Npr3 1083-1140
mod9.12 scripts/MODELLER/SEA1/all_sjkim_final1.py: SEA1 101-275
mod9.12 scripts/MODELLER/SEA1/all_sjkim_final2.py: SEA1 279-473
mod9.12 scripts/MODELLER/SEA1/all_sjkim_final3.py: SEA1 1178-1273
mod9.12 scripts/MODELLER/SEA2/all_sjkim_final1.py: SEA2 127-520
mod9.12 scripts/MODELLER/SEA2/all_sjkim_final2.py: SEA2 1280-1341
mod9.12 scripts/MODELLER/SEA3/all_sjkim_final1.py: SEA3 54-424
mod9.12 scripts/MODELLER/SEA3/all_sjkim_final2.py: SEA3 430-536
mod9.12 scripts/MODELLER/SEA3/all_sjkim_final3.py: SEA3 1092-1139
mod9.12 scripts/MODELLER/SEA4/all_sjkim_final1.py: SEA4 45-426
mod9.12 scripts/MODELLER/SEA4/all_sjkim_final2.py: SEA4 659-835
mod9.12 scripts/MODELLER/SEA4/all_sjkim_final3.py: SEA4 942-1032
Running the IMP/PMI scripts for the SEA complex:
with 1:3 stoichiometry and rotational symmetry:
Author(s): Seung Joong Kim, Riccardo Pellarin, and Peter Cimermancic
Date: October 6th, 2014
License: LGPL. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
- Romain Algret, Javier Fernandez-Martinez, Yi Shi, Seung Joong Kim, Riccardo Pellarin, Peter Cimermancic, Emilie Cochet, Andrej Sali, Brian T. Chait, Michael P. Rout, and Svetlana Dokudovskaya, Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway, Molecular & Cellular Proteomics, 2014, mcp.M114.039388.